Contacts of the helix formed by residues 253 - 271 (chain A) in PDB entry 2HD1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A TYR* 3.5 12.7 - - - -
247A ARG 3.4 19.3 - - - +
248A ASN* 4.6 3.8 - - - +
249A ASN 2.8 25.0 + - - +
250A PRO* 3.3 18.6 + - - +
251A PHE 2.8 14.9 + - - +
252A HIS* 1.3 73.7 - - - +
254A PHE* 1.3 65.6 + - - +
255A ARG* 3.3 11.9 + - - +
256A HIS* 3.0 26.9 + - - +
257A CYS 3.2 8.0 + - - -
416A TRP* 3.9 5.2 - - - -
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Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PRO* 4.3 7.4 - - + -
211A MET* 3.8 40.8 - - + -
212A LEU* 3.6 25.1 - - + -
215A LEU* 3.9 18.4 - - + -
239A LEU* 5.0 1.1 - - + -
242A VAL* 5.0 3.6 - - + -
243A HIS* 3.7 51.4 - + + +
246A TYR* 3.7 25.3 - + + +
247A ARG 4.4 0.6 + - - -
253A ASN* 1.3 75.4 - - - +
255A ARG* 1.3 64.2 + - - +
257A CYS* 3.1 23.8 + - - -
258A PHE* 2.9 21.1 + - + +
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 2.8 34.4 + - + +
204A TRP* 3.5 48.2 + - - +
206A TRP 2.8 30.1 + - - -
207A GLU* 4.8 4.0 - - - +
208A PRO* 5.0 3.8 - - - +
211A MET* 3.8 26.6 - - + +
253A ASN* 3.2 12.7 + - - +
254A PHE* 1.3 79.3 - - - +
256A HIS* 1.3 61.7 + - - +
258A PHE* 3.2 6.8 + - + +
259A CYS* 3.0 29.4 + - - -
416A TRP* 3.8 15.5 - - + -
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A IBM 5.7 0.4 - - - -
101A ZN 2.1 30.3 - - - -
251A PHE* 3.3 46.2 - + - +
252A HIS* 4.3 9.1 - + - -
253A ASN* 3.0 12.0 + - - +
255A ARG* 1.3 77.7 - - - +
257A CYS* 1.3 60.7 + - - +
259A CYS* 3.1 9.3 + - - +
260A VAL* 3.0 35.7 + - + +
292A HIS* 2.9 13.4 + + - -
293A ASP* 2.8 22.9 - - + -
402A ASP* 2.9 26.2 + - - -
405A ASN* 5.0 5.8 + - - -
416A TRP* 3.7 11.3 - - + -
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Residues in contact with CYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 5.0 2.7 - - - -
246A TYR* 3.3 35.2 - - + +
253A ASN 3.2 1.8 + - - -
254A PHE* 3.1 35.3 + - - +
256A HIS* 1.3 79.8 - - - +
258A PHE* 1.3 66.1 + - - +
260A VAL* 3.4 1.6 + - - +
261A ALA* 3.0 24.9 + - - +
289A ALA 4.1 3.8 - - - +
290A ILE* 3.4 29.6 - - - +
292A HIS* 4.3 11.7 - - + -
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Residues in contact with PHE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.0 6.3 - - + -
201A PHE* 3.7 31.4 - + - -
203A VAL* 4.1 26.7 - - + -
206A TRP* 5.0 0.9 - + - -
211A MET* 3.6 45.8 - - + -
214A CYS* 3.5 32.8 - - + -
215A LEU* 3.8 17.0 - - + -
218A MET* 4.2 10.8 - - + -
254A PHE* 2.9 17.6 + - + +
255A ARG* 3.5 8.1 - - + +
256A HIS 3.2 0.2 - - - -
257A CYS* 1.3 79.2 - - - +
259A CYS* 1.3 53.7 + - - +
261A ALA* 3.8 3.5 - - - +
262A GLN* 2.8 42.5 + - + +
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Residues in contact with CYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 3.6 28.7 - - - -
255A ARG* 3.0 21.6 + - - -
256A HIS* 3.3 11.0 - - - +
258A PHE* 1.3 76.5 - - - +
260A VAL* 1.3 61.0 + - + +
262A GLN* 4.5 0.7 - - - -
263A MET* 2.9 18.4 + - - +
401A CYS 4.9 1.3 - - - +
404A SER* 4.7 1.7 + - - +
405A ASN* 4.3 10.1 - - - +
408A ARG* 2.8 35.4 + - - +
416A TRP* 3.5 29.8 - - - -
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A HIS* 3.0 32.7 + - + +
257A CYS 3.8 2.7 - - - +
258A PHE 3.3 0.2 - - - -
259A CYS* 1.3 76.7 - - + +
261A ALA* 1.3 63.4 + - - +
263A MET 3.4 0.2 + - - -
264A MET* 3.0 22.2 + - - +
289A ALA* 3.9 18.2 - - + +
292A HIS* 3.2 34.3 - - + +
398A ILE* 4.6 4.7 - - + +
401A CYS* 3.5 17.3 - - + +
402A ASP* 3.7 30.3 - - + +
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 3.7 17.0 - - + -
218A MET* 4.4 1.8 - - - -
257A CYS 3.0 18.3 + - - +
258A PHE 3.8 0.2 - - - +
260A VAL* 1.3 77.0 - - - +
262A GLN* 1.3 57.4 + - - +
264A MET* 3.2 4.1 + - - +
265A TYR* 2.9 28.6 + - - +
286A MET* 3.8 10.5 - - + +
289A ALA* 3.9 14.7 - - + +
290A ILE* 3.7 28.5 - - + -
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Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 2.9 45.5 + - + +
198A LYS 3.0 22.6 + - - -
199A PRO* 4.8 0.7 - - - +
201A PHE* 3.5 15.4 - - + +
203A VAL* 4.3 0.7 - - - +
218A MET* 3.8 14.5 - - + +
258A PHE* 2.8 35.0 + - + +
259A CYS* 4.0 1.8 - - - +
261A ALA* 1.3 73.6 - - - +
263A MET* 1.3 57.9 + - - +
265A TYR* 3.5 2.9 - - - +
266A SER* 2.8 40.6 + - - -
408A ARG* 2.8 40.7 + - - +
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Residues in contact with MET 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.8 20.4 - - + -
259A CYS 2.9 18.8 + - - +
260A VAL 3.8 3.6 - - - +
261A ALA 3.3 0.2 - - - -
262A GLN* 1.3 73.9 + - - +
264A MET* 1.3 61.1 + - - +
266A SER* 3.2 4.7 + - - -
267A MET* 2.8 36.1 + - + +
400A CYS 5.5 0.2 - - - -
401A CYS* 3.8 13.9 - - + -
404A SER* 3.4 36.6 - - - +
407A VAL* 4.5 5.8 - - + -
408A ARG* 3.6 42.6 - - + +
465A PHE* 6.2 0.2 - - + -
479A MET* 3.4 31.4 - - + -
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Residues in contact with MET 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A VAL 3.0 13.8 + - - +
261A ALA* 3.4 11.4 - - - +
263A MET* 1.3 78.0 - - - +
265A TYR* 1.3 62.2 + - - +
267A MET* 3.1 5.6 + - - +
268A VAL* 2.9 30.0 + - + +
273A LEU* 5.1 8.3 - - - -
285A LEU* 3.8 54.1 - - + +
286A MET* 3.6 19.1 - - - -
289A ALA* 4.5 4.0 - - + -
397A LEU* 3.9 7.0 - - - +
398A ILE* 3.7 35.7 - - + +
401A CYS* 3.4 17.7 - - + -
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Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A ILE 5.0 0.2 + - - -
196A LEU* 3.2 44.9 - - + -
197A ARG* 3.8 12.5 + - + +
217A HIS* 3.6 13.1 + + - -
218A MET* 3.6 41.5 - - + -
221A ASP* 2.5 29.5 + - - +
222A LEU* 4.0 26.7 - - + -
261A ALA 2.9 16.0 + - - +
262A GLN 3.5 4.3 - - - +
264A MET* 1.3 77.2 - - - +
266A SER* 1.3 60.2 + - - +
268A VAL* 3.4 13.7 + - - +
269A TRP* 3.1 47.4 + + - -
286A MET* 4.0 7.8 - - + -
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU 4.1 0.2 + - - -
197A ARG 3.5 19.9 + - - +
198A LYS 3.4 9.2 - - - -
199A PRO* 3.5 18.9 - - - +
262A GLN* 2.8 36.7 + - - -
263A MET* 3.4 16.1 - - - -
264A MET 3.2 0.2 - - - -
265A TYR* 1.3 77.8 - - - +
267A MET* 1.3 58.3 + - - +
269A TRP* 3.2 4.3 + - - +
270A LEU* 2.8 30.1 + - - +
479A MET* 5.5 0.9 - - - -
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Residues in contact with MET 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A MET* 2.8 23.1 + - + +
264A MET* 3.6 9.0 - - - +
266A SER* 1.3 74.7 - - - +
268A VAL* 1.3 60.8 + - - +
270A LEU* 4.1 5.4 - - + -
271A CYS* 2.8 60.0 + - - +
273A LEU* 3.6 9.0 - - + +
397A LEU* 4.5 21.1 - - + -
400A CYS* 4.8 12.8 - - - -
401A CYS* 4.4 15.7 - - - -
465A PHE* 4.9 4.0 - - + -
468A VAL* 5.0 5.6 - - + -
475A VAL* 3.9 9.9 - - + -
479A MET* 3.7 38.1 - - + +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.8 27.8 - - + -
264A MET* 2.9 28.4 + - + +
265A TYR* 3.5 11.0 - - - +
267A MET* 1.3 75.5 - - - +
269A TRP* 1.3 67.1 + - + +
272A SER* 3.0 8.1 + - - -
273A LEU* 2.9 48.4 + - + -
274A GLN* 4.1 22.2 + - + -
282A ILE* 4.4 15.5 - - + -
285A LEU* 5.8 1.8 - - + -
286A MET* 5.1 3.4 - - + -
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Residues in contact with TRP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.5 53.9 - - + +
221A ASP* 3.3 29.4 - - - -
222A LEU* 3.8 21.1 - - + -
265A TYR* 3.1 46.3 + + - -
266A SER 3.2 4.8 + - - +
268A VAL* 1.3 80.2 - - + +
270A LEU* 1.3 65.7 - - - +
272A SER* 3.2 16.7 + - - +
274A GLN* 3.6 26.2 - - + -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A PRO* 5.8 3.4 - - + -
266A SER* 2.8 22.2 + - - +
267A MET* 4.0 3.6 - - + +
269A TRP* 1.3 76.4 - - - +
271A CYS* 1.3 63.0 + - - +
272A SER* 3.6 2.3 + - - -
474A MET* 3.3 36.2 - - + +
475A VAL* 4.1 14.4 - - + -
478A ILE* 3.7 40.6 - - + -
479A MET* 3.8 33.7 - - + -
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Residues in contact with CYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A MET* 2.8 50.8 + - - +
270A LEU* 1.3 76.2 - - - +
272A SER* 1.3 71.1 + - - +
273A LEU* 3.1 13.6 + - + -
276A LYS* 5.0 2.4 - - - +
397A LEU* 5.9 1.3 - - - -
472A PHE* 3.5 43.6 - - + -
474A MET* 4.3 7.9 - - - +
475A VAL* 3.5 20.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il